[gmx-users] gmx mindist error

João Henriques joao.m.a.henriques at gmail.com
Tue Mar 27 15:59:13 CEST 2018

Dear users and developers,

I am trying to use gmx mindist to calculate the minimum distance between
periodic images but I get the following error:

Fatal error:
pbc = no is not supported by g_mindist

This is the command I am running:

gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc

Now, I have to admit that the .xtc file I'm using is generated by ACEMD and
not mdrun, but I used gmx dump to check it and everything looks sane. The
cuboid box sizes are clearly specified and I don't understand what the
problem is...

box (3x3):
   box[    0]={ 8.16756e+00,  0.00000e+00,  0.00000e+00}
   box[    1]={ 0.00000e+00,  8.25175e+00,  0.00000e+00}
   box[    2]={ 0.00000e+00,  0.00000e+00,  9.73586e+00}

Is gmx mindist reading the box vector lengths from the structure file

Thank you for your attention,
Best regards,

More information about the gromacs.org_gmx-users mailing list